Skip to content

Commit

Permalink
Fixup: Drop genotype_nextclade coloring since it is equivalent to min…
Browse files Browse the repository at this point in the history 
…or_lineage
  • Loading branch information
@j23414
j23414 committed Feb 26, 2025
1 parent c0af2c7 commit 8fab9a5
Show file tree
Hide file tree
Showing 3 changed files with 10 additions and 222 deletions.
207 changes: 0 additions & 207 deletions phylogenetic/defaults/color_orderings.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -240,215 +240,8 @@ serotype_genbank denv2
serotype_genbank denv3
serotype_genbank denv4

genotype_nextclade DENV1/I
genotype_nextclade DENV1/II
genotype_nextclade DENV1/III
genotype_nextclade DENV1/IV
genotype_nextclade DENV1/V
genotype_nextclade DENV2/AA
genotype_nextclade DENV2/AI
genotype_nextclade DENV2/AII
genotype_nextclade DENV2/AM
genotype_nextclade DENV2/C
genotype_nextclade DENV2/S
genotype_nextclade DENV3/I
genotype_nextclade DENV3/II
genotype_nextclade DENV3/III
genotype_nextclade DENV3/IV
genotype_nextclade DENV4/I
genotype_nextclade DENV4/II
genotype_nextclade DENV4/S

################
# Hill 2024 dataset
genotype_nextclade 1I
genotype_nextclade 1I_A
genotype_nextclade 1I_B
genotype_nextclade 1I_C
genotype_nextclade 1I_D
genotype_nextclade 1I_E
genotype_nextclade 1I_E.1
genotype_nextclade 1I_E.1.1
genotype_nextclade 1I_E.1.2
genotype_nextclade 1I_E.2
genotype_nextclade 1I_E.3
genotype_nextclade 1I_E.4
genotype_nextclade 1I_F
genotype_nextclade 1I_G
genotype_nextclade 1I_H
genotype_nextclade 1I_H.1
genotype_nextclade 1I_H.2
genotype_nextclade 1I_H.3
genotype_nextclade 1I_J
genotype_nextclade 1I_K
genotype_nextclade 1I_K.1
genotype_nextclade 1I_K.1.1
genotype_nextclade 1I_K.1.2
genotype_nextclade 1I_K.2
genotype_nextclade 1I_K.3
genotype_nextclade 1I_K.4
genotype_nextclade 1I_K.5
genotype_nextclade 1I_K.6
genotype_nextclade 1I_K.7
genotype_nextclade 1II
genotype_nextclade 1III
genotype_nextclade 1III_A
genotype_nextclade 1III_A.1
genotype_nextclade 1III_A.2
genotype_nextclade 1III_A.3
genotype_nextclade 1III_A.4
genotype_nextclade 1III_B
genotype_nextclade 1IV
genotype_nextclade 1IV_A
genotype_nextclade 1IV_B
genotype_nextclade 1IV_B.1
genotype_nextclade 1IV_B.2
genotype_nextclade 1IV_C
genotype_nextclade 1V
genotype_nextclade 1V_A
genotype_nextclade 1V_B
genotype_nextclade 1V_C
genotype_nextclade 1V_D
genotype_nextclade 1V_D.1
genotype_nextclade 1V_D.1.1
genotype_nextclade 1V_D.1.2
genotype_nextclade 1V_D.2
genotype_nextclade 1V_E
genotype_nextclade 1V_E.1
genotype_nextclade 1V_E.2
genotype_nextclade 1V_E.3
genotype_nextclade 1V_E.4
genotype_nextclade 1V_F
genotype_nextclade 1V_G
genotype_nextclade 1V_H
genotype_nextclade 1V_J
genotype_nextclade 1VII
genotype_nextclade 1VII_A
genotype_nextclade 1VII_B
genotype_nextclade 2I
genotype_nextclade 2II
genotype_nextclade 2II_A
genotype_nextclade 2II_A.1
genotype_nextclade 2II_A.1.1
genotype_nextclade 2II_A.1.1.1
genotype_nextclade 2II_A.1.1.2
genotype_nextclade 2II_A.1.2
genotype_nextclade 2II_A.2.1
genotype_nextclade 2II_A.2.2
genotype_nextclade 2II_B
genotype_nextclade 2II_C
genotype_nextclade 2II_C.1
genotype_nextclade 2II_C.2
genotype_nextclade 2II_D
genotype_nextclade 2II_D.1
genotype_nextclade 2II_D.1.1
genotype_nextclade 2II_D.1.2
genotype_nextclade 2II_D.2
genotype_nextclade 2II_D.3
genotype_nextclade 2II_E
genotype_nextclade 2II_E.1
genotype_nextclade 2II_E.2
genotype_nextclade 2II_F
genotype_nextclade 2II_F.1
genotype_nextclade 2II_F.1.1
genotype_nextclade 2II_F.1.1.1
genotype_nextclade 2II_F.1.1.2
genotype_nextclade 2II_F.1.1.3
genotype_nextclade 2II_F.1.1.4
genotype_nextclade 2II_F.1.1.5
genotype_nextclade 2II_F.1.1.6
genotype_nextclade 2II_F.1.2
genotype_nextclade 2II_F.1.3
genotype_nextclade 2II_F.2
genotype_nextclade 2II_F.2.1
genotype_nextclade 2II_F.2.2
genotype_nextclade 2III
genotype_nextclade 2III_A
genotype_nextclade 2III_A.1
genotype_nextclade 2III_A.2
genotype_nextclade 2III_B
genotype_nextclade 2III_C
genotype_nextclade 2III_C.1
genotype_nextclade 2III_C.1.1
genotype_nextclade 2III_C.1.2
genotype_nextclade 2III_C.2
genotype_nextclade 2III_D
genotype_nextclade 2III_D.1
genotype_nextclade 2III_D.1.1
genotype_nextclade 2III_D.1.2
genotype_nextclade 2III_D.1.3
genotype_nextclade 2III_D.2
genotype_nextclade 2III_D.3
genotype_nextclade 2III_E
genotype_nextclade 2IV
genotype_nextclade 2V
genotype_nextclade 2V_A
genotype_nextclade 2V_A.1
genotype_nextclade 2V_A.1.1
genotype_nextclade 2V_A.1.2
genotype_nextclade 2V_A.1.3
genotype_nextclade 2V_A.2
genotype_nextclade 2V_A.3
genotype_nextclade 2V_A.4
genotype_nextclade 2V_B
genotype_nextclade 2V_C
genotype_nextclade 2V_D
genotype_nextclade 2V_E
genotype_nextclade 2VI
genotype_nextclade 3I
genotype_nextclade 3I_A
genotype_nextclade 3I_A.1
genotype_nextclade 3I_A.1.1
genotype_nextclade 3I_A.1.2
genotype_nextclade 3I_A.2
genotype_nextclade 3I_B
genotype_nextclade 3I_C
genotype_nextclade 3II
genotype_nextclade 3II_A
genotype_nextclade 3II_A.1
genotype_nextclade 3II_A.2
genotype_nextclade 3II_A.3
genotype_nextclade 3II_A.4
genotype_nextclade 3II_A.5
genotype_nextclade 3II_B
genotype_nextclade 3III
genotype_nextclade 3III_A
genotype_nextclade 3III_A.1
genotype_nextclade 3III_A.2
genotype_nextclade 3III_B
genotype_nextclade 3III_B.1
genotype_nextclade 3III_B.2
genotype_nextclade 3III_B.3
genotype_nextclade 3III_B.3.1
genotype_nextclade 3III_B.3.2
genotype_nextclade 3III_C
genotype_nextclade 3III_C.1
genotype_nextclade 3III_C.2
genotype_nextclade 3III_C.2.1
genotype_nextclade 3III_C.2.2
genotype_nextclade 3V
genotype_nextclade 4I
genotype_nextclade 4I_A
genotype_nextclade 4I_A.1
genotype_nextclade 4I_A.1.1
genotype_nextclade 4I_A.1.2
genotype_nextclade 4I_A.2
genotype_nextclade 4I_A.3
genotype_nextclade 4I_B
genotype_nextclade 4I_B.1
genotype_nextclade 4I_B.2
genotype_nextclade 4II
genotype_nextclade 4III
genotype_nextclade 4II_A
genotype_nextclade 4II_A.1
genotype_nextclade 4II_A.2
genotype_nextclade 4II_B
genotype_nextclade 4II_B.1
genotype_nextclade 4II_B.1.1
genotype_nextclade 4II_B.1.2
genotype_nextclade 4II_B.2
genotype_nextclade 4IV

genotype 1I
genotype 1II
genotype 1III
Expand Down
10 changes: 5 additions & 5 deletions phylogenetic/defaults/config_dengue.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,11 @@ filter:
traits:
sampling_bias_correction: '3'
traits_columns:
all: 'region serotype_genbank genotype_nextclade'
denv1: 'country region serotype_genbank genotype_nextclade'
denv2: 'country region serotype_genbank genotype_nextclade'
denv3: 'country region serotype_genbank genotype_nextclade'
denv4: 'country region serotype_genbank genotype_nextclade'
all: 'region serotype_genbank'
denv1: 'country region serotype_genbank'
denv2: 'country region serotype_genbank'
denv3: 'country region serotype_genbank'
denv4: 'country region serotype_genbank'

clades:
clade_definitions:
Expand Down
15 changes: 5 additions & 10 deletions phylogenetic/rules/export.smk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,8 @@ rule prepare_auspice_config:
output:
auspice_config="results/defaults/{gene}/auspice_config_{serotype}.json",
params:
replace_clade_key=lambda wildcard: r"clade_membership" if wildcard.gene in ['genome'] else r"genotype_nextclade",
replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"Dengue Genotype (Nextclade)",
replace_clade_key=lambda wildcard: r"clade_membership" if wildcard.gene in ['genome'] else r"major_lineage",
replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"Genotype (Nextclade)",
run:
data = {
"title": "Real-time tracking of dengue virus evolution",
Expand Down Expand Up @@ -79,8 +79,8 @@ rule prepare_auspice_config:
"type": "categorical"
},
{
"key": "genotype_nextclade",
"title": "Dengue Genotype (Nextclade)",
"key": "serotype_genbank",
"title": "Serotype (Genbank metadata)",
"type": "categorical"
},
{
Expand All @@ -97,11 +97,6 @@ rule prepare_auspice_config:
"key": "minor_lineage",
"title": "Minor lineage (Nextclade)",
"type": "categorical"
},
{
"key": "serotype_genbank",
"title": "Serotype (Genbank metadata)",
"type": "categorical"
}
],
"geo_resolutions": [
Expand Down Expand Up @@ -137,7 +132,7 @@ rule prepare_auspice_config:
if wildcards.gene in ['genome'] and wildcards.serotype in ['all']:
clade_membership_title="Serotype (Nextstrain)"
else:
clade_membership_title="Dengue Genotype (Nextstrain)"
clade_membership_title="Genotype (Nextstrain)"

data["colorings"].append({
"key": "clade_membership",
Expand Down

0 comments on commit 8fab9a5

Please sign in to comment.